Airmen with the MQ-9 Aircraft Maintenance Unit, 451st Expeditionary Aircraft Maintenance Squadron perform maintenance work on an MQ-9 Reaper drone, November 2012. Photo: U.S. Air Force

Targeted killing — particularly the sort carried out by the U.S. fleet of deadly flying robots — is a transactional business.

That’s a major point of The Way of The Knife, the informative new book by Mark Mazzetti, a national-security correspondent for the New York Times. The U.S. drone campaign in Pakistan kicked off with the 2004 killing of Nek Mohammed, an extremist in the tribal areas who was not a senior al-Qaida figure. Mohammed was someone the Pakistanis wanted dead. The U.S. wanted access to Pakistan’s airspace and, it was once hoped, western tribal territory, where al-Qaida operated. Over the years, the U.S. got the former and (rarely) the latter, giving birth to a quid pro quo that spread to Yemen and beyond.

That is not to say that Pakistani outrage over targeted killing was entirely fake. The arrest of CIA contractor Raymond Davis in Lahore — where, Mazzetti writes, he was tracking terrorists working with Pakistani intelligence — inflamed the country right before SEALs invaded to kill Osama bin Laden; the Pakistanis view their soil as more inviolable than their airspace. The drone strikes didn’t stop. But they dipped significantly during 2011 and 2012.

That raises an obvious question. When the drone strikes ebb, does it indicate that the CIA and the Joint Special Operations Command are running out of terrorists to target? Or does it indicate merely that the uneasy allies who allow the drones to operate in their territory have revoked cooperation? In the shadow wars that the Bush administration began and the Obama administration proliferated, metrics for success are hard to come by.

Mazzetti’s book, like much of his journalism, provides ground truth that can be sorely lacking as the war on terrorism mutates. And like all trustworthy national-security reporters, he’s a die-hard Yankee fan. Danger Room spoke with Mazzetti on the eve of the publication of The Way of The Knife to find out where the deadly transactions that Washington pursues will send the drones and commandos next.

Danger Room: You explain that the CIA’s covert military operations follow a historical cycle: intensity; exposure; political acrimony; retrenchment; accusations of risk aversion; repeat. Where is the CIA now in this cycle? Or has the Osama bin Laden killing disrupted the cycle?

Mark Mazzetti: Certainly the bin Laden operation was an incredible example of the military and the CIA working closely together on a specific operation, and it brought the CIA a great deal of praise for its work. Roughly two years later though, CIA drone strikes are just now starting to come under public scrutiny, and there will be questions about whether the agency has become too enamored of these remote controlled killings. Up to this point, there has been widespread support among Republicans and Democrats for drone operations, but now members of both parties demanding more transparency and accountability.

I think that this is some of what is driving CIA Director John Brennan’s apparent desire to move some of these paramilitary operations from the CIA to the military. As I talk about in the book, American presidents historically have relied on the CIA as a crutch, ordering covert operations because nobody can figure out a better solution. It’s one of the things that Dennis Blair, the former Director of National Intelligence, warned about before right before he left the Obama administration.

A whole generation of CIA officers have been socialized in war, and so no matter how much Brennan wants to shift the focus of the CIA, I do think it will take a while.

CIA Director John Brennan speaks at an event honoring former Secretary of State Madeleine Albright, March 2012. Photo: CIA

DR: The Way of the Knife explains that the drone strikes in Pakistan arose after Pakistani officials traded access to their airspace for the occasional strike on their enemies. Strikes dipped in 2011 and fell substantially in 2012. Was that because of a lack of remaining targets or because that time period coincided with increased Pakistani acrimony with Washington?

MM: It’s a bit of both. As you point out, the pace of drone strikes in Pakistan has been going down, partly because most of the top layer of al Qaeda leadership is now dead. At the same time, the strikes have also been used to kill off leaders of the Haqqani Network and the Pakistani Taliban.

At the same time, the strikes in 2011 created a great deal of acrimony and were one of several contributing factors to the American-Pakistani relationship becoming toxic. In particular, one strike on March 17, 2011 — the day after CIA contractor Raymond Davis was released from prison — created a tremendous amount of anger both among Pakistani officials and Pakistani citizens.

DR: A major theme of the book is how the CIA spent the 2000s building its military capability while the military spent the 2000s building its spying capability. Is there more convergence now or redundancy?

MM: In the early years after the September 11 attacks, you saw tremendous competition between the CIA and the Pentagon, as both were trying to take charge of the shadow wars. One of the things I write about is how, around 2005-2006, they signed a number of secret arrangements where they “carved up the world” and each took lead responsibility in specific countries. This reduced the instances where the soldiers and spies were tripping over each other in the dark corners of the world, but certainly didn’t end the competition.

To look at a specific case, you see a good deal of redundancy in Yemen. Both the CIA and the Pentagon’s Joint Special Operations Command are running parallel drone wars, and each has their own “kill list.” Because all of the operations in Yemen are shrouded in secrecy, it’s hard to get a good understanding of why two different agencies are running their own secret wars.

DR: Whose idea was it to pay blood money to Pakistanis for the release of CIA contractor Raymond Davis, and what was the broader impact of the Davis episode on CIA’s relationship with Pakistan?

MM: It’s funny, many people have claimed to be the first to come up with the blood money idea. It certainly was discussed both among Pakistani and American officials, and both Pakistani ambassador to Washington Husain Haqqani and General Ahmad Shuja Pasha, the Pakistani spymaster, were instrumental in the arrangement.

It’s hard to overstate how big a deal the Raymond Davis episode still is in Pakistan. When I travelled there last year, I heard far more intense anger about the Davis affair than about the Osama bin Laden raid. For many Pakistanis, it seemed to confirm all the conspiracy theories that the CIA had deployed a secret army into Pakistan to sow violence.

DR: Is it remotely conceivable that the drone war in Pakistan will end after the US withdraws most of its forces from Afghanistan after 2014?

MM: I think that it’s very likely that the drone war in Pakistan will have significantly tapered off by then, since many of the strikes are against groups thought to be doing cross-border attacks on American troops in Afghanistan. However, I would be very surprised if the Obama administration, even after 2014, completely gave up the option of using drones in Pakistan. But, of course Pakistan’s government has a say in that, and depending on where things stand in the relationship next year there is the possibility that Islamabad insists on no more drone strikes.

DR: What are the rules for “signature strikes,” the strikes in Yemen and Pakistan that target military-aged males and not specific, known terrorists?

MM: It’s hard to know the specific rules, because all this remains classified. But I’ve been told that strikes are carried out based on “patterns of activity,” and can be authorized even when the CIA does not know specifically whom they are targeting. Signature strikes are probably the most controversial aspect of the targeted killing program. It’s my understanding that, for instance, a group of males can be targeted based on accumulated evidence that they are engaged in some kind of “militant behavior,” and one example that is often cited is a group of people with guns heading from Pakistan to Afghanistan.

But how exactly can it be determined who is a “military-aged male”? The exact rules of targeting are, at this point, unknown. The botched strike in Pakistan I mentioned earlier, on March 17, 2011, was a signature strike. I have also heard that the drone strike that killed Ilyas Kashmiri, an al-Qaeda leader, was a signature strike.

DR: Did the U.S. deliberately kill Abdulrahman Awlaki, the 16-year old son of Anwar Awlaki? Was it a mistake? And if so, why hasn’t the Obama administration acknowledged killing a teenager and American citizen unconnected to terrorism?

MM: I have not seen or heard anything credible suggesting that Abdulrahman Awlaki was deliberately killed. I believe that it was an egregious mistake, and that the intelligence analysts were trying to target a different person who ended up not being at the outdoor eating spot in Yemen where Abdulrahman was killed.

If the Obama administration had planned to deliberately target a 16-year old American citizen, there would have had to have been a Justice Department opinion authorizing the operation, and I have never heard of any such opinion.

As to why the Obama administration has never discussed the killing, it’s a very good question. I hope that information about the killing is declassified so that we can all know more about what actually happened.

DR: Is there any constituency, with CIA or the Obama administration, to dismantle the killing machine that the CIA has built? Both David Petraeus and Brennan vowed during their confirmation hearings to refocus on traditional spying, but is that a blandishment at this point?

MM: I guess time will tell. Brennan has indicated he wants to move the CIA out of the paramilitary business, and I know that parts of the State Department and Pentagon believe that the CIA shouldn’t be the primary agency doing these killings. But, there is likely to be a strong constituency inside the CIA’s Counterterrorism Center — which really has turned into the beating heart of the CIA since the September 11 attacks — for the CIA to retain at least parts of the drone program.

DR: You quote Richard Blee, a former chief of the CIA bureau that hunted bin Laden, saying, “If we are going to hand down death sentences, there ought to be some public accountability and some public discussion about the whole thing.” Would the CIA actually accept such a thing, since it would potentially expose the CIA to legal jeopardy?

MM: The CIA is always worried about future prosecutions for past actions, so certainly there would be a concern. The danger would be greater internationally than domestically. Despite being a poorly-kept secret, drone strikes are a “covert action,” which means they are authorized by a secret presidential finding. But, obviously, presidential findings have no jurisdiction overseas, so there is the possibility that other countries or international organizations might try to bring prosecutions.

DR: What’s more likely: the battered, aged Yankees make the postseason; or the Obama administration actually ends the shadow wars that it’s proliferating deeper into Africa?

MM: Spencer, thanks for saving the hardest question for the end! I can’t believe I’m devoted to a baseball team whose starting lineup resembles the cast of “Cocoon,” and no doubt my patience will be tried all season. I’m going to call that one a “push.”